I have been doing a ton of work on a huge town and city mixed with an extensive quest-line, but there are quite a lot of dirty things with the mod because it was mostly created when the editor just came out and was extremely buggy. I was wondering if it was possible to transfer just my modified cells over to a new fresh clean mod and leave everything else behind so I can re-create all the quests and scripts but in a much more clean way.

Also is it still better to do the mod in an ESM + ESP format do to all the issues with the editor or have most of them been fixed? There will be a lot of NPC interaction and AI.

Thanks,
Natfoth

Using an ESM nowadays isn't required as a solution to certain bugs/problems. Most of those issue's have been resolved. Unless you are adding HUGE worldspace an ESM shouldn't be necessary.

There is a trick to copying into new plugins. I vaguely remember reading something of the procedure.

Make a new empty plugin and load it as the active plugin alongside your old one. Simply make duplicates of all the cells you wish to keep, save the plugin. Close the CK and remove your old plugin from Skyrim/Data.

I could be wrong, as I think there is more to it than that, make sure to backup your old plugin.

Well I have a ton of actual terrain edits as well in the 3-4 cells is why I cannot just duplicate the buildings, anyway to copy the landscape over also?

Not sure about exteriors. Maybe 3rd party tools like TES5Edit have this capability? User's like JustinOther or Arthmoor would be good people to ask about this.